The intrinsic dimension of protein sequence evolution

It is well known that, in order to preserve its structure and function, a protein cannot change its sequence at random, but only by mutations occurring preferentially at specific locations. We here investigate quantitatively the amount of variability that is allowed in protein sequence evolution, by computing the intrinsic dimension (ID) of the sequences belonging to a selection of protein families. The ID is a measure of the number of independent directions that evolution can take starting from a given sequence. We find that the ID is practically constant for sequences belonging to the same family, and moreover it is very similar in different families, with values ranging between 6 and 12. These values are significantly smaller than the raw number of amino acids, confirming the importance of correlations between mutations in different sites. However, we demonstrate that correlations are not sufficient to explain the small value of the ID we observe in protein families. Indeed, we show that the ID of a set of protein sequences generated by maximum entropy models, an approach in which correlations are accounted for, is typically significantly larger than the value observed in natural protein families. We further prove that a critical factor to reproduce the natural ID is to take into consideration the phylogeny of sequences

Utjecaj sadržaja D vitamina i fosfata u hrani na apsorpciju kalcija i stroncija iz probavnog trakta

The effect of various amounts of phosphates and vitamin D in the diet on calcium and strontium absorption was studied in rats. The animals were kept on experimental diet for 6 days and during that period they received radioactive isotopes of calcium (45Ca) and strontium (85Sr) in drinking water. Skeletal retention of radioactive calcium and strontium was determined. Increased dietary phosphates (from 0.5 to 1.2% P) were found to cause a reduction in the retention of radioactive calcium and strontium after oral administration of isotopes. The effect of phosphates proved to be much stronger on strontium than on calcium absorption. This is in agreement with our earlier results. The effect of phosphates on calcium and strontium metabolism proved independent of the vitamin D content in the diet if this content ranged from 200 to 800 I. U. per 100 g of dry food.Istraživali smo djelovanje različitih količina fosfata i D vitamina u hrani štakora na apsorpciju stroncija i kalcija iz probavnog trakta. Štakori su 6 dana bili na određenom dijetnom režimu, i u to su vrijeme primali radioaktivne izotope kalcija i stroncija (45Ca i 85Sr) oralnim putem. Odredili smo retenciju radioaktivnog kalcija i stroncija u skeletu. Povišeni sadržaj fosfata u hrani (od 0.5 na 1.2% P) izaziva sniženje apsorpcije radioaktivnog kalcija i stroncija iz probavnog trakta. Fosfati djelu i u znatno jače na metabolizam stroncija negoli kalcija. Ti su nalazi u skladu s našim ranijim rezultatima. Spomenuti efekti fosfata na metabolizam kalcija i stroncija nezavisni su od količine D vitamina u hrani ukoliko ona raste od 200 do 800 i. j. na 100 g suhe hrane

X-ray analysis of the proper motion and pulsar wind nebula for PSR J1741-2054

We obtained six observations of PSR J1741-2054 using the $Chandra$ ACIS-S detector totaling $\sim$300 ks. By registering this new epoch of observations to an archival observation taken 3.2 years earlier using X-ray point sources in the field of view, we have measured the pulsar proper motion at $\mu =109 \pm 10 {\rm mas\ yr}^{-1}$ in a direction consistent with the symmetry axis of the observed H$\alpha$ nebula. We investigated the inferred past trajectory of the pulsar but find no compelling association with OB associations in which the progenitor may have originated. We confirm previous measurements of the pulsar spectrum as an absorbed power law with photon index $\Gamma$=2.68$\pm$0.04, plus a blackbody with an emission radius of (4.5$^{+3.2}_{-2.5})d_{0.38}$ km, for a DM-estimated distance of $0.38d_{0.38}$ kpc and a temperature of $61.7\pm3.0$ eV. Emission from the compact nebula is well described by an absorbed power law model with a photon index of $\Gamma$ = 1.67$\pm$0.06, while the diffuse emission seen as a trail extending northeast of the pulsar shows no evidence of synchrotron cooling. We also applied image deconvolution techniques to search for small-scale structures in the immediate vicinity of the pulsar, but found no conclusive evidence for such structures.Comment: 7 pages, 8 figures, 4 Tables; Accepted by Ap

Novel synthesis of benzimidazole by Ring Contraction Rearrangement of benzodiazepine

Condensation of substituted aromatic ketones (acetophenone) and substituted aldehydes give unsaturated ketones 14 (chalcones) which react with o-phenylenediamine 7 to afford the corresponding benzodiazepines 15. Treatments of benzodiazepines under basic conditions give benzimidazole derivatives. Structures of all synthesized compounds have been characterized by their NMR and mass spectral data.Keywords: N’-Thioacylamidines, Chalcone, o-phenylenediamine, benzodiazepine, benzimidazole

Deep Chandra Observations of the Pulsar Wind Nebula Created by PSR B0355+54

We report on Chandra X-ray Observatory (CXO) observations of the pulsar wind nebula (PWN) associated with PSR B0355+54 (eight observations with a 395 ks total exposure, performed over an 8 month period). We investigated the spatial and spectral properties of the emission coincident with the pulsar, compact nebula (CN), and extended tail. We find that the CN morphology can be interpreted in a way that suggests a small angle between the pulsar spin axis and our line-of-sight, as inferred from the radio data. On larger scales, emission from the 7' (2 pc) tail is clearly seen. We also found hints of two faint extensions nearly orthogonal to the direction of the pulsar's proper motion. The spectrum extracted at the pulsar position can be described with an absorbed power-law + blackbody model. The nonthermal component can be attributed to magnetospheric emission, while the thermal component can be attributed to emission from either a hot spot (e.g., a polar cap) or the entire neutron star surface. Surprisingly, the spectrum of the tail shows only a slight hint of cooling with increasing distance from the pulsar. This implies either a low magnetic field with fast flow speed, or particle re-acceleration within the tail. We estimate physical properties of the PWN and compare the morphologies of the CN and the extended tail with those of other bow shock PWNe observed with long CXO exposures.Comment: 11 pages, 8 figure

Combining Charlson and Elixhauser scores with varying lookback predicated mortality better than using individual scores

Objective: To investigate variation in the presence of secondary diagnosis codes in Charlson and Elixhauser comorbidity scores and assess whether including a 1-year lookback period improved prognostic adjustment by these scores individually, and combined, for 30-day mortality. Study Design and Setting: We analyzed inpatient admissions from January 1, 2007 to May 18, 2018 in Oxfordshire, UK. Comorbidity scores were calculated using secondary diagnostic codes in the diagnostic-dominant episode, and primary and secondary codes from the year before. Associations between scores and 30-day mortality were investigated using Cox models with natural cubic splines for nonlinearity, assessing fit using Akaike Information Criteria. Results: The 1-year lookback improved model fit for Charlson and Elixhauser scores vs. using diagnostic-dominant methods. Including both, and allowing nonlinearity, improved model fit further. The diagnosis-dominant Charlson score and Elixhauser score using a 1-year lookback, and their interaction, provided the best comorbidity adjustment (reduction in AIC: 761 from best single score model). Conclusion: The Charlson and Elixhauser score calculated using primary and secondary diagnostic codes from 1-year lookback with secondary diagnostic codes from the current episode improved individual predictive ability. Ideally, comorbidities should be adjusted for using both the Charlson (diagnostic-dominant) and Elixhauser (1-year lookback) scores, incorporating nonlinearity and interactions for optimal confounding control

Ontogeny of hallucal metatarsal rigidity and shape in the rhesus monkey (Macaca mulatta) and chimpanzee (Pan troglodytes)

Life history variables including the timing of locomotor independence, along with changes in preferred locomotor behaviors and substrate use during development, influence how primates use their feet throughout ontogeny. Changes in foot function during development, in particular the nature of how the hallux is used in grasping, can lead to different structural changes in foot bones. To test this hypothesis, metatarsal midshaft rigidity [estimated from the polar second moment of area (J) scaled to bone length] and cross-sectional shape (calculated from the ratio of maximum and minimum second moments of area, Imax /Imin ) were examined in a cross-sectional ontogenetic sample of rhesus macaques (Macaca mulatta; n = 73) and common chimpanzees (Pan troglodytes; n = 79). Results show the hallucal metatarsal (Mt1) is relatively more rigid (with higher scaled J-values) in younger chimpanzees and macaques, with significant decreases in relative rigidity in both taxa until the age of achieving locomotor independence. Within each age group, Mt1 rigidity is always significantly higher in chimpanzees than macaques. When compared with the lateral metatarsals (Mt2-5), the Mt1 is relatively more rigid in both taxa and across all ages; however, this difference is significantly greater in chimpanzees. Length and J scale with negative allometry in all metatarsals and in both species (except the Mt2 of chimpanzees, which scales with positive allometry). Only in macaques does Mt1 midshaft shape significantly change across ontogeny, with older individuals having more elliptical cross-sections. Different patterns of development in metatarsal diaphyseal rigidity and shape likely reflect the different ways in which the foot, and in particular the hallux, functions across ontogeny in apes and monkeys

Data on a new beta titanium alloy system reinforced with superlattice intermetallic precipitates

The data presented in this article are related to the research article entitled “a new beta titanium alloy system reinforced with superlattice intermetallic precipitates” (Knowles et al., 2018) [1]. This includes data from the as-cast alloy obtained using scanning electron microscopy (SEM) and x-ray diffraction (XRD) as well as SEM data in the solution heat treated condition. Transmission electron microscopy (TEM) selected area diffraction patterns (SADPs) are included from the alloy in the solution heat treated condition, as well as the aged condition that contained < 100 nm B2 TiFe precipitates [1], the latter of which was found to exhibit double diffraction owing to the precipitate and matrix channels being of a similar width to the foil thickness (Williams and Carter, 2009) [2]. Further details are provided on the macroscopic compression testing of small scale cylinders. Of the micropillar deformation experiment performed in [1], SEM micrographs of focused ion beam (FIB) prepared 2 µm micropillars are presented alongside those obtained at the end of the in-situ SEM deformation as well as videos of the in-situ deformation. Further, a table is included that lists the Schmidt factors of all the possible slip systems given the crystal orientations and loading axis of the deformed micropillars in the solution heat treated and aged conditions